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App improvements for production #16

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App improvements for production #16

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dbc5390
reorg Dockerfile
gadenbuie Jul 17, 2019
5fdd14c
Remove choice of particular BioMart mirror
gadenbuie Jul 17, 2019
92c4a28
Add caching of data queries and plots
gadenbuie Jul 17, 2019
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8 changes: 4 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -16,16 +16,16 @@ RUN Rscript -e "BiocManager::install(c('haploR', 'HiTC', 'Sushi', 'biomaRt'))" \
RUN Rscript -e "install.packages(c('writexl', 'plotly', 'shinyWidgets'))" \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds

RUN Rscript -e "install.packages(c('ggpubr'))" \
RUN Rscript -e "install.packages(c('ggpubr', 'digest'))" \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds

ARG SHINY_APP_IDLE_TIMEOUT=0
RUN sed -i "s/directory_index on;/app_idle_timeout ${SHINY_APP_IDLE_TIMEOUT};/g" /etc/shiny-server/shiny-server.conf

RUN rm -r /srv/shiny-server/* && mkdir -p /srv/shiny-server/epiTAD/data
COPY VERSION /srv/shiny-server/epiTAD
COPY data/ /srv/shiny-server/epiTAD/data/
COPY www/ /srv/shiny-server/epiTAD/www/
COPY global.R /srv/shiny-server/epiTAD
COPY ui.R /srv/shiny-server/epiTAD
COPY server.R /srv/shiny-server/epiTAD
COPY data/ /srv/shiny-server/epiTAD/data/
COPY www/ /srv/shiny-server/epiTAD/www/
COPY VERSION /srv/shiny-server/epiTAD
2 changes: 1 addition & 1 deletion global.R
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Expand Up @@ -21,7 +21,7 @@ logger <- function(...) {

# Global Data
logger("Connecting to BioMart: ensembl, hsapiens_gene_ensemble")
ensembl54 <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl",mirror = "useast")
ensembl54 <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl")
logger("Loading cached HiC Data")
load("data/hicData.Rdata")

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